##################################
#                                #
# Last modified 06/24/2012       # 
#                                #
# Georgi Marinov                 #
#                                # 
##################################

import sys
import string

def run():

    if len(sys.argv) < 2:
        print 'usage: python %s fasta outputfilename' % sys.argv[0]
        sys.exit(1)

    fasta = sys.argv[1]
    outfilename = sys.argv[2]

    outfile = open(outfilename, 'w')
    
    inputdatafile = open(fasta)
    ID=''
    for line in inputdatafile:
        if line[0]=='>':
            if ID == '':
                ID = line.strip().split('>')[1]
            else:
                sequence = ''.join(sequence)
                contigs = sequence.split('N')
                for contig in contigs:
                    if contig != '':
                       C+=1
                       outfile.write('>' + ID + '_contig_' + str(C) + '\n')
                       outfile.write(contig + '\n')
                ID = line.strip().split('>')[1]
            C=0
            sequence=[]
        else:
            sequence.append(line.strip())   

    sequence = ''.join(sequence)
    contigs = sequence.split('N')
    for contig in contigs:
        if contig != '':
            C+=1
            outfile.write('>' + ID + '_contig_' + str(C) + '\n')
            outfile.write(contig + '\n')
   
run()